How do I install the Hisat2 Extract Snps Haplotypes Vcf Py skill?

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vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Hisat2 Extract Snps Haplotypes Vcf Py by vimalinx

Name: Hisat2 Extract Snps Haplotypes Vcf Py
Rating: 4.666666666666667 (3 reviews)
Author: vimalinx

File contents

hisat2-extract-snps-haplotypes-vcf-py

Quick Start

Command: hisat2_extract_snps_haplotypes_VCF.py <genome_file> <VCF_fnames> <base_fname>
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2_extract_snps_haplotypes_VCF.py
Full reference: See references/help.md

When To Use This Tool

Use hisat2_extract_snps_haplotypes_VCF.py when your variants are already in VCF and you need HISAT2 graph-index inputs.
It is appropriate for genome-, chromosome-, or gene-oriented reference builds where VCF-derived SNP/haplotype extraction is required.
Use it instead of the UCSC extractor whenever the source data is generic VCF rather than UCSC SNP tables.
Reach for --extra-files if you also want auxiliary .ref and _backbone.fa outputs for downstream inspection or genotyping workflows.

Common Patterns

# Convert one VCF into HISAT2 SNP and haplotype files
hisat2_extract_snps_haplotypes_VCF.py genome.fa variants.vcf.gz hg38_vcf

# Combine multiple VCFs via a comma-separated argument
hisat2_extract_snps_haplotypes_VCF.py genome.fa cohort1.vcf.gz,cohort2.vcf.gz hg38_vcf

# Change reference scale and emit extra backbone/reference files
hisat2_extract_snps_haplotypes_VCF.py genome.fa variants.vcf.gz hg38_vcf --reference-type chromosome --extra-files

# Allow non-rs identifiers and print extraction statistics
hisat2_extract_snps_haplotypes_VCF.py genome.fa variants.vcf.gz hg38_vcf --non-rs -v

Recommended Workflow

Prepare a genome FASTA file (e.g., genome.fa) and VCF file(s) containing variant data
Run extraction: hisat2_extract_snps_haplotypes_VCF.py genome.fa variants.vcf output_base
Tune --inter-gap (default: 30) and --intra-gap (default: 50) to control haplotype grouping
Use output files as input for HISAT2 graph index building

Guardrails

VCF files can be plain text or gzipped; multiple files are comma-separated
SNP IDs must begin with "rs" unless --non-rs is specified
Use --verbose to monitor extraction statistics during processing
Output is keyed by base_fname and writes at least .snp and .haplotype; --extra-files additionally produces .ref and _backbone.fa
This helper does not implement --version; use -h/--help instead

---name: hisat2-extract-snps-haplotypes-vcf-pydescription: Use when extracting SNPs and haplotypes from VCF files to build variant-aware HISAT2 graph genome indexes--- # hisat2-extract-snps-haplotypes-vcf-py ## Quick Start - **Command**: `hisat2_extract_snps_haplotypes_VCF.py <genome_file> <VCF_fnames> <base_fname>` - **Local executable**: `/home/vimalinx/miniforge3/envs/bio/bin/hisat2_extract_snps_haplotypes_VCF.py` - **Full reference**: See [references/help.md](references/help.md) ## When To Use This Tool - Use `hisat2_extract_snps_haplotypes_VCF.py` when your variants are already in VCF and you need HISAT2 graph-index inputs. - It is appropriate for genome-, chromosome-, or gene-oriented reference builds where VCF-derived SNP/haplotype extraction is required. - Use it instead of the UCSC extractor whenever the source data is generic VCF rather than UCSC SNP tables. - Reach for `--extra-files` if you also want auxiliary `.ref` and `_backbone.fa` outputs for downstream inspection or genotyping workflows. ## Common Patterns ```bash # Convert one VCF into HISAT2 SNP and haplotype files hisat2_extract_snps_haplotypes_VCF.py genome.fa variants.vcf.gz hg38_vcf # Combine multiple VCFs via a comma-separated argument hisat2_extract_snps_haplotypes_VCF.py genome.fa cohort1.vcf.gz,cohort2.vcf.gz hg38_vcf # Change reference scale and emit extra backbone/reference files hisat2_extract_snps_haplotypes_VCF.py genome.fa variants.vcf.gz hg38_vcf --reference-type chromosome --extra-files # Allow non-rs identifiers and print extraction statistics hisat2_extract_snps_haplotypes_VCF.py genome.fa variants.vcf.gz hg38_vcf --non-rs -v ``` ## Recommended Workflow 1. Prepare a genome FASTA file (e.g., `genome.fa`) and VCF file(s) containing variant data 2. Run extraction: `hisat2_extract_snps_haplotypes_VCF.py genome.fa variants.vcf output_base` 3. Tune `--inter-gap` (default: 30) and `--intra-gap` (default: 50) to control haplotype grouping 4. Use output files as input for HISAT2 graph index building ## Guardrails - VCF files can be plain text or gzipped; multiple files are comma-separated - SNP IDs must begin with "rs" unless `--non-rs` is specified - Use `--verbose` to monitor extraction statistics during processing - Output is keyed by `base_fname` and writes at least `.snp` and `.haplotype`; `--extra-files` additionally produces `.ref` and `_backbone.fa` - This helper does not implement `--version`; use `-h/--help` instead

Frequently asked questions